Butremycin, the 3-hydroxyl derivative of ikarugamycin and a protonated aromatic tautomer of 5'-methylthioinosine from a Ghanaian Micromonospora sp. K310.

A new actinomycete strain Micromonospora sp. K310 was isolated from Ghanaian mangrove river sediment. Spectroscopy-guided fractionation led to the isolation of two new compounds from the fermentation culture. One of the compounds is butremycin (2) which is the (3-hydroxyl) derivative of the known Streptomyces metabolite ikarugamycin (1) and the other compound is a protonated aromatic tautomer of 5'-methylthioinosine (MTI) (3). Both new compounds were characterized by 1D, 2D NMR and MS data. Butremycin (2) displayed weak antibacterial activity against Gram-positive S. aureus ATCC 25923, the Gram-negative E. coli ATCC 25922 and a panel of clinical isolates of methicillin-resistant S. aureus (MRSA) strains while 3 did not show any antibacterial activity against these microbes.

Lechevalieria nigeriaca sp. nov., isolated from arid soil.

A novel actinobacterium, designated strain NJ2035(T), was isolated from soil collected from Abuja, Nigeria and was characterized to determine its taxonomic position. The isolate was found to have chemical and morphological properties associated with members of the genus Lechevalieria. Phylogenetic analyses based on almost-complete 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Lechevalieria, and was shown to form a distinct phyletic line in the Lechevalieria phylogenetic tree. Strain NJ2035(T) was most closely related to Lechevalieria roselyniae C81(T), Lechevalieria atacamensis C61(T) and Lechevalieria deserti C68(T) (98.5 % 16S rRNA gene sequence similarity). Sequence similarities with other members of the genus Lechevalieria were less than 98.2 %. The cell wall of the novel strain contained meso-diaminopimelic acid, and galactose, mannose and rhamnose as the diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. DNA-DNA relatedness and phenotypic data showed that the novel isolate and L. roselyniae C81(T), L. atacamensis C61(T) and L. deserti C68(T) belong to distinct genomic species. On the basis of data from this taxonomic study using a polyphasic approach, strain NJ2035(T) represents a novel species of the genus Lechevalieria, for which the name Lechevalieria nigeriaca sp. nov. is proposed. The type strain is NJ2035(T) ( = DSM 45680(T) = KCTC 29057(T) = NRRL B-24881(T)).

Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine.

A novel halotolerant actinomycete, designated strain BNT52(T), was isolated from soil collected from Cihanbeyli Salt Mine in the central Anatolia region of Turkey, and examined using a polyphasic taxonomic approach. The isolate was found to have chemical and morphological properties typical of the genus Amycolatopsis and formed a distinct phyletic line in the 16S rRNA gene tree. Strain BNT52(T) was most closely related to Amycolatopsis nigrescens CSC17Ta-90(T) (96.7 %), Amycolatopsis magusensis KT2025(T) (96.6 %), Amycolatopsis sulphurea DSM 46092(T) (96.6 %), Amycolatopsis dongchuanensis YIM 75904(T) (96.5 %), Amycolatopsis ultiminotia RP-AC36(T) (96.4 %) and Amycolatopsis sacchari DSM 44468(T) (96.4 %). Sequence similarities with other strains of species of the genus Amycolatopsis were lower than 96.2 %. The isolate grew at 20-37 °C, pH 6-12 and in the presence of 0-10 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids were iso-C16 : 0 2-OH and iso-C16 : 0. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylmethylethanolamine. The genomic DNA G+C content was 68.8 mol%. On the basis of the data from this polyphasic taxonomic study, strain BNT52(T) represents a novel species within the genus Amycolatopsis for which the name Amycolatopsis cihanbeyliensis sp. nov. is proposed (type strain BNT52(T) = KCTC 29065(T) = NRRL B-24886(T) = DSM 45679(T)).

Saccharomonospora amisosensis sp. nov., isolated from deep marine sediment.

A novel actinomycete, strain DS3030(T), was isolated from a deep sediment sample, collected from the southern Black Sea coast, Turkey, and was examined using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain DS3030(T) was shown to belong to the genus Saccharomonospora and to be related most closely to Saccharomonospora marina XMU15(T) (99.6 % similarity). Sequence similarities with other strains of the genus Saccharomonospora were lower than 97.0 %. The organism had chemical and morphological features typical of the genus Saccharomonospora. The cell wall of the novel strain contained meso-diaminopimelic acid, arabinose and galactose as diagnostic sugars. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone was MK-9(H4). Major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH and C16 : 1cis 9. Phenotypic data clearly distinguished the new isolate from its closest relative, S. marina XMU15(T). The combined genotypic and phenotypic data and low DNA-DNA relatedness with its closest related strain reveal that strain DS3030(T) represents a novel species of the genus, for which the name Saccharomonospora amisosensis sp. nov. is proposed. The type strain is DS3030(T) ( = DSM 45685(T) = KCTC 29069(T) = NRRL B-24885(T)).

Methylobacterium tarhaniae sp. nov., isolated from arid soil.

A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211(T), isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211(T) belonged to the genus Methylobacterium. Strain N4211(T) was most closely related to Methylobacterium aquaticum GR16(T) (98.56 %), Methylobacterium platani PMB02(T) (97.95 %) and Methylobacterium variabile GR3(T) (97.2 %), and the phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C18 : 1 cis11/t9/t6). The DNA G+C content was 67.3 mol%. DNA-DNA relatedness of strain N4211(T) and the most closely related strains M. aquaticum DSM 16371(T) and M. platani KCTC 12901(T) were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA-DNA hybridization data, strain N4211(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium tarhaniae sp. nov. is proposed. The type strain is N4211(T)( = KCTC 23615(T) = DSM 25844(T)).

Nonomuraea jabiensis sp. nov., isolated from arid soil.

A novel actinomycete, strain A4036(T), was isolated from a soil sample collected from the Jabi district in Abuja, Nigeria. The taxonomic position of strain A4036(T) was established using a combination of genotypic and phenotypic analyses. The organism formed extensively branched substrate and aerial hyphae that generated spiral chains of spores with warty surfaces. The cell wall contained meso-diaminopimelic acid and the cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinone was MK-9(H(4)). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylinositol mannoside, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, two unidentified phospholipids and four unknown glucosamine-containing phospholipids. The major cellular fatty acids were iso-C(16 : 0) 2-OH, iso-C(16 : 0) and 10-methyl C(17 : 0). On the basis of 16S rRNA gene sequence similarity studies, strain A4036(T) grouped in the genus Nonomuraea, being most closely related to Nonomuraea angiospora IFO 13155(T) (99.05 %), Nonomuraea candida HMC10(T) (98.78 %), Nonomuraea kuesteri GW 14-1925(T) (98.49 %), Nonomuraea endophytica YIM 65601(T) (98.42 %), Nonomuraea maheshkhaliensis 16-5-14(T) (98.40 %), Nonomuraea turkmeniaca DSM 43926(T) (98.38 %), Nonomuraea helvata IFO 14681(T) (98.29 %), Nonomuraea rubra DSM 43768(T) (98.10 %) and Nonomuraea salmonea DSM 43678(T) (98.06 %). Levels of 16S rRNA gene sequence similarity to the type strains of other species of the genus Nonomuraea were <98 %. Despite the high 16S rRNA gene sequence similarities, DNA-DNA relatedness values and phenotypic data demonstrated that strain A4036(T) was clearly distinguished from all closely related species of the genus Nonomuraea. Thus, this isolate is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea jabiensis sp. nov. is proposed. The type strain is A4036(T) (= DSM 45507(T) = KCTC 19870(T)).

Amycolatopsis magusensis sp. nov., isolated from soil.

A novel actinomycete, designated strain KT2025(T), was isolated from arid soil collected from Magusa, northern Cyprus. The taxonomic position of the novel strain was established by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Amycolatopsis. Phylogenetic analyses based on 16S rRNA gene sequences supported the classification of the isolate in the genus Amycolatopsis and showed that the organism formed a cluster with Amycolatopsis nigrescens CSC17-Ta-90(T), Amycolatopsis minnesotensis 32U-2(T), Amycolatopsis sacchari DSM 44468(T) and Amycolatopsis dongchuanensis YIM 75904(T). 16S rRNA gene sequence similarity analysis indicated that strain KT2025(T) was most closely related to Amycolatopsis lurida DSM 43134(T) (97.5 %), Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409(T) (97.4 %), Amycolatopsis keratiniphila subsp. nogabecina DSM 44586(T) (97.1 %), Amycolatopsis nigrescens DSM 44992(T) (97.1 %), Amycolatopsis azurea DSM 43854(T) (97.1 %) and Amycolatopsis minnesotensis DSM 44988(T) (96.9 %). The organism was found to have chemical features typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and hydroxy-phosphatidylethanolamine. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the genomic DNA was 70.8 mol%. Phenotypic data clearly distinguished the isolate from its closest relatives. The combined genotypic and phenotypic data and low levels of DNA-DNA relatedness with its closest relatives indicated that strain KT2025(T) represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis magusensis sp. nov. is proposed. The type strain is KT2025(T) ( = DSM 45510(T) = KCTC 29056(T)).

The variation of antioxidant defense system of Streptomyces sp. M4018 with respect to carbon sources.

The effect of glycerol, glucose, and starch as carbon sources on the antioxidant defense system such as superoxide dismutase (SOD) and catalase (CAT) activities, pyruvate levels, and membrane lipid peroxidation (LPO) levels of Streptomyces sp. M4018, after isolation from the rhizosphere samples of Colutea arborescens and identification as a strain of S. hiroshimensis based on phenotypic and genotypic characteristics, were investigated. As an antioxidant defense enzyme, SOD activities increased up to 20 g/L of glycerol and 15 g/L of starch, while they showed negative correlation with glucose concentration. CAT activity variations of glycerol- and glucose-supplemented mediums showed significant positive correlations with the trend of SOD activities. However, CAT activity, in contrast to SOD, in Streptomyces sp. M4018 tended to decrease as the starch concentration increased. The production of pyruvate increased with respect to glycerol and starch up to 15 g/L, while it was positively correlated with glucose concentration. The highest pyruvate production was seen at 20 g/L glucose. Membrane LPO levels were negatively correlated with the activities of SOD and CAT enzymes, and the minimum LPO level was determined at 5 g/L of glucose, where SOD and CAT activities reached their maximum levels. Nevertheless, the higher SOD and CAT activities in a wider range of incubation period compared to the beginning by resulting in insignificant increases in membrane LPO levels showed the unusual antioxidant response capacities of the in Streptomyces sp. M4018 against the potentially deleterious effects of reactive oxygen species (ROS) for glycerol, glucose, and starch as carbon sources.

Streptosporangium anatoliense sp. nov., isolated from soil in Turkey.

A novel actinobacterium, strain N9999(T), was isolated from soil and its taxonomic position determined using a polyphasic approach. The organism formed abundant aerial hyphae that differentiated into spherical spore vesicles. The cell wall contained meso-diaminopimelic acid; the whole-cell sugars were galactose, glucose, mannose, madurose and ribose; the predominant menaquinones MK-9 (H(2)) and MK-9 (H(4)); the major phospholipids phosphatidylethanolamine, diphosphatidylglycerol, a phosphaglycolipid and phosphatidylinositol mannosides; while the cellular fatty acids were rich in iso-C(14:0), C(15:0), cis-9-C(17:1), iso-C(16:0) and 10-methyl C(17:0) components. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence indicated that strain N9999(T) was closely related to a group that consisted of Streptosporangium pseudovulgare DSM 43181(T) and Streptosporangium nondiastaticum DSM 43848(T). However, DNA-DNA relatedness and phenotypic data demonstrated that strain N9999(T) was clearly distinguished from all closely related Streptosporangium species. The combined genotypic and phenotypic data demonstrate conclusively that the isolate should be classified as a new species of Streptosporangium.

Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil.

A novel actinobacterial strain, A4029T, isolated from arid soil of Abuja, Nigeria, and provisionally assigned to the genus Actinoplanes, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence similarity studies showed that strain A4029T belonged to the genus Actinoplanes, being most closely related to Actinoplanes brasiliensis DSM 43805T (98.9 %) and Actinoplanes deccanensis DSM 43806T (98.0 %); similarity to other type strains of the genus Actinoplanes ranged from 96.2 to 97.9 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol; characteristic sugars arabinose and xylose; major fatty acids iso-C15:0, anteiso-C15:0, iso-C16:0, C17:1ω9c and iso-C14:0] confirmed the affiliation of strain A4029T to the genus Actinoplanes. The results of DNA-DNA hybridizations and phylogenetic analysis, together with phenotypic and biochemical test data, allowed strain A4029T to be differentiated from strains of other Actinoplanes species. Therefore, strain A4029T represents a novel species, for which the name Actinoplanes abujensis sp. nov. is proposed, with A4029T (=DSM 45518T=NRRL B-24835T=KCTC 19984T) as the type strain.

Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil.

The taxonomic position of two soil actinomycetes, strains A2012(T) and A2019(T), isolated from Turkish soils, was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the strains belonged to the family Nocardiaceae. Strains A2012(T) and A2019(T) were most closely related to Nocardia caishijiensis DSM 44831(T) (98.9 %) and Nocardia mexicana CIP 108295(T) (98.6 %), respectively; similarity to other type strains of the genus Nocardia ranged from 96.9 to 97.9 %. However, DNA-DNA relatedness and phenotypic data demonstrated that strains A2012(T) and A2019(T) could be clearly distinguished from members of the most closely related Nocardia species. It is evident from the genotypic and phenotypic data that the two isolates represent two novel species of the genus Nocardia. It is proposed, therefore, that strains A2012(T) and A2019(T) be classified in the genus Nocardia as representatives of Nocardia goodfellowii sp. nov. (type strain A2012(T) = DSM 45516(T) = NRRL B-24833(T) = KCTC 19986(T)) and Nocardia thraciensis sp. nov. (type strain A2019(T) = DSM 45517(T) = NRRL B-24834(T) = KCTC 19985(T)), respectively.

Actinomadura geliboluensis sp. nov., isolated from soil.

A novel actinobacterium, strain A8036(T), isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H(6)) and MK-9(H(4)). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C(16:0), C(17:1)cis9, C(16:0), C(15:0) and 10-methyl C(17:0). Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036(T) were Actinomadura meyerae DSM 44715(T) (99.23% similarity), Actinomadura bangladeshensis DSM 45347(T) (98.9%) and Actinomadura chokoriensis DSM 45346(T) (98.3%). However, DNA-DNA relatedness and phenotypic data demonstrated that strain A8036(T) could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036(T) is therefore considered to represent a novel species of the genus Actinomadura, for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036(T) ( = DSM 45508(T) = KCTC 19868(T)).

Williamsia limnetica sp. nov., isolated from a limnetic lake sediment.

An actinomycete, strain L1505(T), was isolated from a limnetic lake sediment and found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with its classification in the genus Williamsia. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain L1505(T) formed a distinct lineage within the genus Williamsia. The isolate belonged to a cluster containing W. muralis MA140/96(T), W. marianensis MT8(T) and W. faeni N1350(T), with which the isolate shared 99.0-98.2 % 16S rRNA gene sequence similarity. Genotypic and phenotypic data also indicated that the isolate was different from known members of the genus Williamsia. On the basis of these data, strain 1505(T) is considered to represent a novel species of the genus Williamsia, for which the name Williamsia limnetica sp. nov. is proposed (type strain L1505(T) = DSM 45521(T) = NRRL B-24829(T) = KCTC 19981(T)).

Carbohydrate metabolite pathways and antibiotic production variations of a novel Streptomyces sp. M3004 depending on the concentrations of carbon sources.

To determine the variations of growth, some key enzyme activities such as glucose kinase (GK), glucose-6-phosphate dehydrogenase (G6PDH), α-ketoglutarate dehydrogenase (KGDH), and isocitrate lyase (ICL) besides metabolite levels of pyruvate and antibiotic production of newly isolated Streptomyces sp. M3004 were grown in culture media which contain 10-20 g/l concentration with either glucose or glycerol as carbon source. Biomass and intracellular glucose and glycerol levels of Streptomyces sp. M3004 showed positive correlation with the concentration of these carbon sources, and these levels were higher in glucose compared with the glycerol-supplemented mediums. GK, G6PDH, and KGDH activities showed marked correlation with the concentration of both glucose and glycerol, and the activity levels were 4.14-, 1.47-, and 1.27-fold higher in glucose than glycerol. A key enzyme of the glyoxalate cycle, ICL activities decreased with increasing glucose concentrations from 10 to 20 g/l, but increased up to 15 g/l of glycerol. The positive correlations were also determined between intracellular glucose and glycerol levels besides pyruvate and protein variations with respect to concentrations of the carbon sources. Antibacterial activities of Streptomyces sp. M3004 reached maximum on the stationary phase, while it did not change significantly with respect to glucose and glycerol.

The correlations between TCA-glyoxalate metabolite and antibiotic production of Streptomyces sp. M4018 grown in glycerol, glucose, and starch mediums.

The alterations of organic acids citrate, α-ketoglutarate, succinate, fumarate, malate production together with isocitrate lyase activity as a glyoxalate shunt enzyme, and antibiotic production of Streptomyces sp M4018 were investigated in relation to changes in the glucose, glycerol and starch concentrations (5-20 g/L) after identification as a strain of Streptomyces hiroshimensis based on phenotypic and genotypic characteristics. The highest intracellular citrate and α-ketoglutarate levels in 20 g/l of glucose, glycerol, and starch mediums were 399.47 ± 4.78, 426.93 ± 6.40, 355.84 ± 5.38 ppm and 444.81 ± 5.12, 192.96 ± 2.26, 115.20 ± 2.87 ppm, respectively. The highest succinate, malate, and fumarate levels were also determined in 20 g/l of glucose medium as 548.9 ± 11.21, 596.15 ± 8.26, and 406.42 ± 6.59 ppm and the levels were significantly higher than the levels in glycerol and starch. Extracellular organic acid levels measured also showed significant correlation with carbon source concentrations by showing negative correlation with pH levels of the growth medium. The antibiotic production of Streptomyces sp. M4018 was also higher in glucose medium as was the case also for organic acids when compared with glycerol. On the other hand, there is no production in starch.

Streptomyces samsunensis sp. nov., a member of the Streptomyces violaceusniger clade isolated from the rhizosphere of Robinia pseudoacacia.

The taxonomic position of a Streptomyces isolate, strain M1463(T), recovered from the rhizosphere of Robinia pseudoacacia was established in a polyphasic study. The organism had chemical and morphological markers that were consistent with its classification in the Streptomyces violaceusniger clade. This assignment was confirmed by 16S rRNA gene sequence data, which also showed that the strain formed a distinct subclade together with Streptomyces malaysiensis DSM 41697(T). However, the two strains were readily distinguished on the basis of DNA relatedness and phenotypic data. The combined genotypic and phenotypic data show that strain M1463(T) should be recognized as a representative of a novel species in the Streptomyces violaceusniger clade, for which the name Streptomyces samsunensis sp. nov. is proposed. The type strain of S. samsunensis is M1463(T) ( = DSM 42010(T) = NRRL B-24803(T)).